Genome-wide association studies and functional annotation of pre-weaning calf mortality and reproductive traits in Nellore cattle from experimental selection lines.

Background: Reproductive efficiency is crucial for the long-term economic sustainability of beef cattle production. Pregnancy loss and stillbirth are complex reproductive traits that do not yet have their genomic background fully understood, especially in zebu breeds (Bos taurus indicus). Hence, this study aimed to perform a genome-wide association study (GWAS) and functional annotation for conception success (CS), pregnancy loss (PL), stillbirth (SB), and pre-weaning calf mortality (PWM) in Nellore cattle.

Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population.

Background: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR).

Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations.

Nellore cattle () is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT).

Effects of inbreeding on production traits and genetic evaluations in Guzerá beef cattle raised under tropical conditions.

The objectives of this study were to evaluate the influence of inbreeding on growth traits and body measurements, as well as on the estimation of genetic parameters and genetic trends in Guzerá cattle. Phenotypic records of 4,212 animals selected for postweaning weight from Guzerá Breeding Program of Advanced Beef Cattle Research Center were utilized. The pedigree file contained records from 7,213 animals born from 1928 to 2019.

Benchmarking machine learning and parametric methods for genomic prediction of feed efficiency-related traits in Nellore cattle.

Genomic selection (GS) offers a promising opportunity for selecting more efficient animals to use consumed energy for maintenance and growth functions, impacting profitability and environmental sustainability. Here, we compared the prediction accuracy of multi-layer neural network (MLNN) and support vector regression (SVR) against single-trait (STGBLUP), multi-trait genomic best linear unbiased prediction (MTGBLUP), and Bayesian regression (BayesA, BayesB, BayesC, BRR, and BLasso) for feed efficiency (FE) traits. FE-related traits were measured in 1156 Nellore cattle from an experimental breeding program genotyped for ~ 300 K markers after quality control.

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle.

Background: Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world.

Relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls: a cross sectional study.

The aim of this study was to investigate the relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls selected for postweaning weight. Data from the andrological evaluation of 836 bulls born between 2000 and 2019, including 583 Nellore animals (Bos indicus) and 253 Caracu animals (Bos taurus), were used. The bulls were divided into categories of age at the time of assessment: category 1 consisted of animals aged 20 to 23 months (22 ± 0.

Muscle growth affects the metabolome of the pectoralis major muscle in red-winged tinamou (Rhynchotus rufescens).

The aim of the present study was to identify and quantify the metabolites (metabolome analysis) of the pectoralis major muscle in male red-winged tinamou (Rhynchotus rufescens) selected for growth traits. A selection index was developed for females [body weight (BW), chest circumference (CC), and thigh circumference (TC)] and males [BW, CC, TC, semen volume, and sperm concentration] in order to divide the animals into 2 experimental groups: selection group with a higher index (TinamouS) and commercial group with a lower index (TinamouC). Twenty male offspring of the 2 groups (TinamouS, n = 10; TinamouC, n = 10) were confined for 350 d.

Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions.

The prenatal environment is recognized as crucial for the postnatal performance in cattle. In tropical regions, pregnant beef cows commonly experience nutritional restriction during the second half of the gestation period. Thus, the present study was designed to analyze the genotype by prenatal environment interaction (G × Epn) and to identify genomic regions associated with the level and response in growth and reproduction-related traits of beef cattle to changes in the prenatal environment.

Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups.

The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls.

Effects of Feeding and Drinking Behavior on Performance and Carcass Traits in Beef Cattle.

Feed and water efficiency are important traits to improve beef cattle production’s economic and environmental sustainability. This study evaluated residual feed intake (RFI) and residual water intake (RWI) and their relationship with performance, ingestive behavior, and carcass traits in Caracu beef cattle. The data were analyzed using a generalized linear model with least squares means.

Use of auxiliary techniques for assessing the reproductive capacity of natural service Nellore bulls.

The aim of this study was to investigate whether parameters obtained by computer-assisted sperm analysis (CASA), infrared thermography (IRT), and testicular B-mode and Doppler ultrasound can be used as indicators of fertility in natural service Nellore bulls. Twenty-nine Nellore bulls were evaluated on days 66 (-D66), 38 (-D38), and 10 (-D10) before the beginning of natural service mating. In all assessments, semen samples were collected and sperm kinetics were evaluated by CASA, thermographic imaging of the scrotal and ocular region, testicular B-mode ultrasound, and Doppler ultrasound of the spermatic cord.

Growth performance, reproductive parameters and fertility measures in young Nellore bulls with divergent feed efficiency.

The growth, sexual maturity and fertility-related parameters related of young Nellore bulls with divergent residual feed intake (RFI) raised on pasture were evaluated. After classification of 48 young males as low and high RFI (more and less efficient, respectively), the animals were evaluated for growth and reproductive parameters at 28-day intervals from 14.3 to 24.

Improving the accuracy of beef cattle methane inventories in Latin America and Caribbean countries.

On-farm methane (CH) emissions need to be estimated accurately so that the mitigation effect of recommended practices can be accounted for. In the present study prediction equations for enteric CH have been developed in lieu of expensive animal measurement approaches. Our objectives were to: (1) compile a dataset from individual beef cattle data for the Latin America and Caribbean (LAC) region; (2) determine main predictors of CH emission variables; (3) develop and cross-validate prediction models according to dietary forage content (DFC); and (4) compare the predictive ability of these newly-developed models with extant equations reported in literature, including those currently used for CH inventories in LAC countries.

Analysis of residual feed intake in Nellore bulls of different ages, rib eye area, and backfat thickness.

The aim of the present study was to use different models that include body composition phenotypes for the evaluation of residual feed intake (RFI) in Nellore bulls of different ages. Phenotypic and genotypic data of bulls that had participated in feed efficiency tests of a commercial (COM) and an experimental (EXP) herd between 2007 and 2019 were used. The mean entry age in the two herds was 645 and 279 days, respectively.

socialh: An R package for determining the social hierarchy of animals using data from individual electronic bins.

Cattle have a complex social organization, with negative (agonistic) and positive (affiliative) interactions that affect access to environmental resources. Thus, the social behaviour has a major impact on animal production, and it is an important factor to improve the farm animal welfare. The use of data from electronic bins to determine social competition has already been validated; however, the studies used non-free software or did not make the code available.

Performance and muscle lipogenesis of calves born to Nellore cows with different residual feed intake classification.

This study aimed to evaluate relationships among maternal residual feed intake (RFI) with growth performance and expression of genes involved in lipid metabolism in offspring of Nellore cattle. Fifty-three cows classified as negative or positive RFI by genomic prediction were exposed to fixed-time artificial insemination (FTAI) protocols at 2 and 3 years of age using semen from the same bull. In the first year, cows gestated under grazing conditions and nursed their calves in the feedlot.

Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits.

Background: Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI).

Effect of Nellore (Bos indicus) donor age on in-vitro embryo production and pregnancy rate.

The aim of this study was to evaluate the effect of age of Nellore (Bos indicus) donors on the efficiency of in vitro embryo production (IVEP) and pregnancy rate. Thirty-six donors, including 11 female calves (13 ± 0.61 months), 17 prepubertal heifers (25 ± 0.

Phenotypic association among performance, feed efficiency and methane emission traits in Nellore cattle.

Enteric methane (CH4) emissions are a natural process in ruminants and can result in up to 12% of energy losses. Hence, decreasing enteric CH4 production constitutes an important step towards improving the feed efficiency of Brazilian cattle herds. The aim of this study was to evaluate the relationship between performance, residual feed intake (RFI), and enteric CH4 emission in growing Nellore cattle (Bos indicus).

Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions.

The objectives of this study were to measure the relative expression of the ATP1A1, NR3C1, POMC, NPY, and LEP genes in Caracu (Bos taurus) and Nelore (Bos indicus) bulls submitted to feed efficiency tests at high environmental temperatures, and to evaluate differences in adaptability to tropical conditions between breeds. Thirty-five Caracu and 30 Nelore bulls were submitted to a feed efficiency test using automated feeding stations. At the end of the test, the animals were subjected to thermoneutral (TN) and heat stress (HS) conditions.

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers.

Background: Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI).

Different selection practices affect the environmental sensitivity of beef cattle.

The objective of the present study was to evaluate the effects of different selection practices on the environmental sensitivity of reproductive and growth traits in males and females of three Nellore selection lines [control (NeC), selection (NeS), and traditional (NeT) lines]. Moreover, genetic trends for the intercept and slope were estimated for each line, and the possible reranking of sires was examined. A total of 8,757 records of selection weight (SW), 3,331 records of scrotal circumference (SC), and 2,311 records of days to first calving (DFC) from Nellore cattle born between 1981 and 2017 were analyzed.